MolNFT v1 · #54015 · protein
Factor xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor
2XC4 · Activated factor xa heavy chain: “Factor xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor”. X-ray diffraction, 3 ligands (IVK, CA, NA), 4 pockets (best druggability 0.48). MolNFT v1 #54015 on GenesisL1: 3D structure…
- PDB
- 2XC4
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activated factor xa heavy chain; Factor X light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- IVK, CA, NA
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activated factor xa heavy chain (EC 3.4.21.6) | protein | 233 | 13% helix, 37% strand | P00742 |
| L | Factor X light chain (EC 3.4.21.6) | protein | 54 | 7% helix, 26% strand | P00742 |
Ligands and binding sites
- IVK · (3R,4R)-N-(4-chlorophenyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-1-(2,2,2-trifluoroethyl)pyrrolidine-3,4-dicarboxamide · ligand · chains A
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.48 | 0.79 | 23 | IVK |
| 2 | 153 | 0.45 | 0.76 | 26 | empty |
| 3 | 51 | 0.34 | 0.79 | 16 | empty |
| 4 | 54 | 0.33 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–L · 913 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2XC4 · Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00742
- Elsewhere: RCSB PDB 2XC4 · PDBe 2XC4 · UniProt P00742
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.